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Index of Documents Provided by the Federal Bureau of Investigation1 BATCH 1 Module 1: Technical Review Panel Meetings Technical Review Panels 1. November 5, 2001 WFO Anthrax Expert Panel Review (pp. 2-27) 2. December 7, 2001 External Technical Review Panel (pp. 28-39) 3. December 12, 2001 External Review of Analytical Plan (pp. 40-46) 4. June 11-12, 2002 Progress to Date Review (pp. 47-65) 5. August 8, 2005 Chemistry Review Panel (pp. 66-195) Module 2: USAMRIID Initial examination of the letter spore preparations for physical characteristics (microscopy and electron microscopy) and spore viability studies. 1. 18 Oct 2001 SPS02.57 (Daschle) CFU Report (p. 3) 2. 21 Oct 2001 EM Report of Dasch1e Letter (pp. 4-19) 1 The Committee on the Review of the Scientific Approaches Used During the FBI’s Investigation of the 2001 Bacillus anthracis Mailings initially received FBI materials related to the science of the Anthrax Mailings Investigation in two batches. A third batch of documents was provided later. In addition to the documents in the three principal batches of materials, the FBI also provided several supplemental documents in response to committee requests. Unless otherwise noted, this index reflects the order in which the materials were received from the FBI, the manner in which the documents were organized by the FBI, and the language used by the FBI when describing the documents. Page numbers in parentheses after document titles are the page numbers assigned to the document by the FBI or, in cases where the FBI did not assign page numbers, the number of pages in the respective document. 161

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162 SCIENTIFIC APPROACHES USED TO INVESTIGATE THE ANTHRAX LETTERS 3. 24 Oct 2001 SPS02.88.1 (NY Post) CFU Report (pp. 20-21) 4. 25 Oct 2001 EM Daschle “Si” Report (pp. 22-25) 5. 25 Oct 2001 Simons Letter re NY Post (pp. 26-28) 6. 28 Oct 2001 EM/CFU Report of NY Post (p. 29) 7. 27 Nov 2001 Report on Isolates from Daschle and NY Post Letters (p. 30) Special Pathogens Sample Test Laboratory Analytical Test Reports: Results of Analysis of Letter Material 8. SPS.02.88 NY Post Powder 10/22/2001 (pp. 32-33) 9. SPS.02.44 Brokaw Envelope 11/4/2001 (pp. 34-35) 10. SPS.02.57 Daschle Letters and Powders 11/9/2001 (pp. 36-45) 11. SPS.02.266 Leahy Powder (pp. 46-53) Microbiological examinations and identification of phenotypic variants (Mor- photypes) which appeared different than the predominant “Ames” phenotype 12. Report #1 Analysis of Evidentiary Material (pp. 55-68) 13. Report #2 Analysis of Repository Samples (pp. 69-79) 14. Report #3 Analysis of Environmental Samples - AMI (pp. 80-90) 15. Report #4 Examination of Repository Spore Preparations: Screening for the Hemolytic B. subtilis Contaminant (pp. 91-95) 16. Report #5 Analysis of Repository Samples (pp. 96-99) Isolation of Morphological Variants from FBI Repository Samples FBIR 049 004 (Leahy) PowerPoint Photos 17. Isolation of Morphological Variants from FBI Repository Samples FBIR 049 004 (Leahy) PowerPoint Photos (pp. 101-109) Module 3: Ames Strain Identification Reports 1. Forensic Analysis of Putative Anthrax Samples, Batch E0001 v02.01.02 (MLVA-8) (pp. 3-10) 2. MLVA-15 Molecular Typing (Batch E0001) 4/16/02 (pp. 11-14) 3. Laboratory Reports NAU-0001 (May 30, 2002) to NAU-0038 (May 5, 2008) (pp. 15-167)

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163 INDEX OF DOCUMENTS PROVIDED BY THE FBI Guidelines and Standard Operating Procedures 4. Guidelines and Standard Operating Procedures for Forensic Analysis V09.2303 (pp. 168-204) 5. Guidelines and Standard Operating Procedures for Forensic Analysis: Real-Time PCR species Specific, Canonical and Strain Specific SNP Genotyping of Bacillus anthracis and Francisella tularensis V11.03.04 (pp. 206-231) 6. Real-Time PCR species Specific, Canonical and Strain Specific SNP Genotyping of Bacillus anthracis V04.11.07 (pp. 232-272) 7. Quality Assurance Standards for Forensic DNA Analysis (pp. 273-280) Literature 8. “Multiple-Locus Variable-Number Tandem Repeat Analysis Reveals Genetic Relationships within Bacillus anthracis” (Keim et al., 2000, 182:2928-2936) (pp. 282-291) Progress Reports 9. NAU DNA-Based Strain Typing of Anthrax Samples (pp. 293-649)2 Module 4: Analysis for Evidence of Genetic Engineering Reports 1. 19 October 2001 LANL Receipt letter (pp. 3-4) 2. Laboratory Reports (pp. 5-55) Presentation 3. Analysis of the Amerithrax B. Anthracis Ames Isolates for Evidence of Genetic Engineering (pp. 57-79) Module 5: Genomic Sequencing Publications 1. “Global Genetic Population Structure of Bacillus anthracis,” M. Van Ert et al., (2007) PLoS ONE 2(5); e461. doil-. 1371/jpornal. pone.0000461 (pp. 2-11) 2 The FBI did not assign a name to this document. The descriptor was assigned by the committee.

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164 SCIENTIFIC APPROACHES USED TO INVESTIGATE THE ANTHRAX LETTERS 2. “The Complete Genome Sequence of Bacillus anthracis Ames ‘Ancestor,’” J. Ravel et al, J. Bacteriology, Jan 2009, Vol 191, No. 1, p. 445-446 (pp. 12-13) Reports 3. Genomic Analysis of Bacillus anthracis Isolates Relevant to the Amerithrax Investigation, June 1, 2004 (Morph A, B, C, D, Wild type) (pp. 17-75) 4. Genomic Analysis of Bacillus anthracis Isolates Relevant to the Amerithrax Investigation, June 4, 2005 (Morph E (Opaque, Post/ Leahy B.s.) (pp. 76-159) 5. Multiple Locus PCR-based Assay for the Direct Comparison of unknown B. subtilis isolates to B. Subtilis, New York Post, May 15, 2006 (pp. 160-220) TIGR Progress Reports 6. TIGR Progress Reports (pp. 221-458) Module 6: Sandia National Laboratory (SNL) Reports 1. Sandia National Laboratory Final Report (pp. 3-42) Historical Literature 2. “Distribution of Calcium and Other Elements in Cryosectioned Bacillus cereus T Spores, determined by High-Resolution Scanning Electron Probe X-Ray Microanalysis,” M. Stewart, A.P. Somlyo, A.V. Somlyo, H. Shuman, J.A. Lindsay, W.G. Murrell, J .Bacteriology, July 1980, Vol 143, No. 1, pp. 481-491 (pp. 44-54) 3. “Scanning Electron Probe X-Ray Microanalysis of Elemental Distribution in Freeze-Dried Cryosections of Bacillus coagulans Spores.” M. Stewart, A.P. Somlyo, A.V. Somlyo, H. Shuman, J.A. Lindsay, W.G. Murrell, J . Bacteriology, Aug. 1981, Vol 147, No. 2, pp. 670-674 (pp. 55-59) 4. “Automated Analysis of SEM X-Ray Spectral Images: A Powerful New Microanalysis Tool,” P.G. Kotula, M.R. Kennan, J.R. Michael, Microsc. Microanal., 9, 1-17, 2003 (pp. 60-76) 5. Silicon Summary Bibliography of Select Publications (pp. 77-81)

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165 INDEX OF DOCUMENTS PROVIDED BY THE FBI PowerPoint Files of Individual Sample Results 6. PowerPoint Files of Individual Sample Results (pp. 82-532) Module 7: Chemistry Unit, FBI Laboratory FBI Laboratory Reports 1. 020322006 April 15, 2002 Q13 SPS02.88 (Post) (pp. 3-4) 2. 020605001 June 18, 2002 Q12 White Powder (Leahy) (pp. 5-6) 3. 020110004 August 26, 2002 Q12, Bc 14579, Bs/Ba+/ (pp. 7-10) 4. 020605001 October 16, 2002 Q13 SPS02.88 Elemental (pp. 11-12) 5. 040624018 June 28, 2004 Leahy Powder Elemental (pp. 13-14) 6. 030519001 October 15, 2003 Culture Media Elemental (pp. 15-22) 7. 031008001 October 30, 2003 Burans 12 Elemental (pp. 23-25) 8. 031124029 December 11, 2003 10 DPG growths Elemental (pp. 26-28) 9. 030819015 June 29, 2004 Commercial Media (pp. 29-34) 10. 050321004 April 18, 2005 Media Salts and Spores (pp. 35-37) 11. 050118006 April 18, 2005 19 DPG Stubs SEM (pp. 38-54) 12. 050408005 May 18, 2005 2 DPG Stubs SEM (pp. 55-67) 13. 050408005 July 6, 2005 2 DPG Stubs SEM (pp. 68-91) Elemental Analysis Summary 14. 1 Elemental Analysis Summary Table (pp. 93-94) 15. Comparison of results from 2 different instruments (by 2 different FBI examiners, 2 years apart in 2 different Labs (HQ VS Quantico) Envelopes and Particle Transport 16. FBI Laboratory Electron Microscopy of Envelope surfaces and particle transport thru envelopes (pp. 96-111) Module 8: Carbon-14 (14C) Dating Center for Accelerator Mass Spectrometry (CAMS), Lawrence Livermore National Laboratory

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166 SCIENTIFIC APPROACHES USED TO INVESTIGATE THE ANTHRAX LETTERS 1. CAMS background information (pp. 3-14) 2. Proposal (pp. 15-16) 3. Quantitating Radiocarbon Concentrations in Isolated Samples of Biological Origin: Standard Operating Procedures for FBI Measurements of Natural 14C (pp. 17-23) 4. LLNL Report 10/14/02 (pp. 24-29) 5. LLNL Report 1/16/04 Addendum (pp. 30-33) 6. LLNL Data Table 3/30/04 DPG Samples (pp. 34-39) 7. Scientific References (pp. 40-50) National Ocean Sciences Accelerator Mass Spectrometry Facility (NOSAMS), Woods Hole Oceanographic Institute 8. NOSAMS background information (pp. 52-55) 9. General Statement of C-14 Procedures (pp. 56-57) 10. Amerithrax Sample Handling Procedures (pp. 58-72) 11. Final Report (pp. 73-83) 12. Scientific References (pp. 84-112) Module 9: Stable Isotopes Stable Isotope Reports 1. Isotopic Characterization of Water Samples 3/14/03 (pp. 3-10) 2. Isotopic Characterization of Anthrax Samples 7/30/03 (pp. 11-19) 3. Isotopic Characterization of Water Samples 10/15/03 (pp. 20-25) 4. Isotopic Characterization of Spore Samples 1/5/04 (pp. 26-31) 5. Stable Isotope Characterization of Anthrax Sample SPS 02.266 2/22/04 (pp. 32-44) 6. Isotopic Characterization of Microbial Spore Samples 5/20/04 (pp. 45-53) 7. A Report on the Stable Isotope Ratios of Envelope Samples 9/17/04 (pp. 54-58) 8. A Report on the Stable Isotope Ratios of Treated and Untreated Envelopes 11/7/04 (pp. 59-64) 9. A Report on the Stable Isotope Ratios of Treated and Untreated Envelopes 12/22/04 (pp. 65-77) 10. Isotopic Characterization of RMR 1029 5/6/05 (pp. 78-80) 11. A Tabulation of Stable Isotopes of Tap Water Samples Analyzed for the FBI 3/23/05 (pp. 81-247) Proposals and SOWS 12. Proposals and SOWS (pp. 248-269)

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167 INDEX OF DOCUMENTS PROVIDED BY THE FBI Kreuzer-Martin Publications 13. Kreuzer-Martin Publications (pp. 271-310) Stable Isotope Ratios and the Forensic Analysis of Microorganisms PowerPoint 14. Stable Isotope Ratios and the Forensic Analysis of Microorganisms PowerPoint (pp. 312-342) Module 10: Agar and Heme Analysis Agar Assay University of Maryland 1. Unsolicited Proposal SOW (pp. 3-8) 2. Progress Reports (pp. 9-55) 3. Summary of Chromatograms (pp. 56-72) 4. Final Agar Report (pp. 73-94) 5. Reductive Hydrolysis Procedure Steps (pp. 95-96) 6. Reductive Hydrolysis Literature References (pp. 97-118) 7. ASMS Abstract Poster (pp. 119-120) Agar Assay Validation - BMI 8. Task 4 Spot Report 27 Aug 2002 (pp. 122-126) 9. Task 4 Interim Report 17 Sept 2002 (pp. 127-136) Heme Assay (UMD) 10. SOW (pp. 138-149) 11. Progress Reports (pp. 150-182) 12. Analysis of Heme by MALDI Procedure (pp. 183-190) 13. Filter Sterilization Validation (pp. 191-192) 14. Heme Final Report (pp. 193-216) 15. Heme A.C. publication (pp. 217-222) Heme Assay Validation – ECBC 16. Interim Report (ECBC) (pp. 224-238) 17. Analytical Test Report (ECBC) (10 Aug 2005) (pp. 239-246) Agar Overview 18. Agar Overview (pp. 248-251)

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168 SCIENTIFIC APPROACHES USED TO INVESTIGATE THE ANTHRAX LETTERS Module 11: Pacific Northwest National Laboratory Reports 1. Residual Agar Determination in Bacterial Cultures by ESI/MS, DHS Final Report (pp. 3-99) 2. Detection of Agar, by Analysis of Sugar Markers, Wunschel et al., J. Microbiol Methods, 74, (2008), 57-63 (pp. 101-107) 3. Residual Agar Determination in Bacterial Cultures by ESI/MS, K.L. Wahl et al. submitted for publication (pp. 108-141) Presentation 4. FBI Samples Data Summary PowerPoint (pp. 143-197) Module 12: FBI Laboratory Renocal Assay Reports 1. FBI Lab Report 070829018 (pp. 2-3) Standard Operating Procedures 2. Meglumine Diatrizoate Analysis by LC/MS/ESI (pp. 5-26) 3. Performance Monitoring Protocol (QA/QC) for the Finnigan LTQ LC/MS (ESI) Instrument (pp. 27-45) Reference 4. Detection of Trace Amounts of Meglumine and Diatizoate from Bacillus Spore Samples Using Liquid Chromatography/Mass Spectrometry; submitted to Anal. Chem. (pp. 47-74) Module 13: DPG Production Methods Test Plan 1. Test Plan (pp. 3-24) Project Overview PowerPoint 2. Project Overview PowerPoint (pp. 26-60)

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169 INDEX OF DOCUMENTS PROVIDED BY THE FBI Final Report Dated 2/1/06 3. Final Report Dated 2/1/06 (pp. 62-118) SEM Photos of Production 4. SEM Photos of Production (pp. 120-255) Module 14: Preparation of B. anthracis Ames on Commercial and Prepared Media Report 1. Preparation of B. anthracis Ames Spores on Commercially Prepared Media and Media Prepared at USAMRIID (pp. 3-6) BATCH 2 Module 1: B. Subtilis Contaminant Battelle 1. Report of isolation of contaminant from Brokaw letter in “Summary of Microbiological Analysis 19 Oct 2001” (pp. 3-5) Centers for Disease Control 2. Report of identification of contaminant submitted by BMI as B. subtilis including morphology, hemolysis, gram staining, antibiotic resistance and 16s rRNA sequence match (pp. 7-19) Novazymes 3. Identification of the NY Post contaminant as B. licheniformis (p. 21) Applied Biosystems 4. Identification of the B. subtilis isolated from the Brokaw and NY Post letters by 16s ribosomal RNA gene sequence analysis (pp. 23-32)

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170 SCIENTIFIC APPROACHES USED TO INVESTIGATE THE ANTHRAX LETTERS TIGR Genomic Analysis of Bacillus anthracis Isolates Relevant to the Amerithrax Investigation, June 4, 2005 (Morph E (Opaque), Post/ Leahy B.s.) (see Batch 1, Module 5, Document 3) Multiple Locus PCR-based Assay for the Direct Comparison of Unknown B. subtilis Isolates to B. subtilis, New York Post, May 15, 2006 (see Batch 1, Module 5, Document 4) Module 2: Whole Genome Assembly of B. subtilis Isolate Technical Proposals and SOW 1. Microbial Genetic Services in Support of the Amerithrax Investigation (FBI SOW) (pp. 3-42) 2. Whole Genome Assembly, Closure Annotation of Bacillus subtilis GB22 (TO1) (pp. 43-57) 3. Multiple Locus PCR-Based Assay of the Direct Comparison of One Unknown B. subtilis Isolate to B. subtilis New York Post (TO3) (pp. 58-74) 4. Training for Use of Affymetrix Comparative Genomic Hybridization Arrays (TO4) (pp. 75-91) 5. Develop an Annotation File Specific to the FBI B. Subtilis Comparative Genomic Hybridization Arrays (New TO5) (pp. 92-101) Progress Reports 6. Whole Genome Assembly, Closure and Annotation of Bacillus subtilis GB2212/07-4/08 (TO1) (pp. 103-106) 7. Multiple Locus PCR-based Assay of the Direct Comparison of One Unknown B. subtilis Isolate to B. subtilis New York Post 1/08-4/08 (TO3) (pp. 107-114) 8. Multiple locus PCR-Based Assay of the Direct Comparison of One Unknown B. subtilis Isolate to B. subtilis New York Post 5/08 (TO3) (pp. 115-122) Standard Operating Procedures 9. Affymetrix GB22 Tiling GeneChip SOP (pp. 124-136)

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171 INDEX OF DOCUMENTS PROVIDED BY THE FBI Final Reports 10. Whole Genome Assembly, Closure and Annotation of Bacillus subtilis GB22 (TO1) (pp. 138-142) 11. Multiple Locus PCR-Based Assay of the Direct Comparison of One Unknown B. subtilis Isolate to B. subtilis New York Post (TO3) (pp. 143-166) 12. Genome MTV Manual (TO4) (pp. 167-185) Module 3: Genetic Diversity and Phylogenetic Characterization of B. subtilis Statement of Work (SOW) 1. Genetic Diversity and Phylogenetic Characterization of B. subtilis (pp. 3-14) Progress Reports 2. 8 Monthly and 1 Quarterly Report 12/06-11/07 (pp. 16-79) Standard Operating Procedures 3. Allele-Specific Oligonucleotide (ASO) Typing Assay for Bacillus subtilis (pp. 81-82) Final Reports 4. Genetic Diversity and Phylogenetic Characterization of B. subtilis 11/30/07 (pp. 84-124) Module 4: B. subtilis Screening Standard Operating Procedures 1. Bacillus subtilis Analysis by Singleplex Real-Time PCR Standard Operating Procedure (pp. 3-10) Synopsis of Assay Development 2. Synopsis of Assay Development (pp. 11-55)

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172 SCIENTIFIC APPROACHES USED TO INVESTIGATE THE ANTHRAX LETTERS Standard Operating Procedures 3. Analytical Plan, Acceptance of Work (AOW) 40 (pp. 57-104) Analytical Plans 4. Analytical Plan, Acceptance of Work (AOW) 46 (pp. 106-115) 5. Analytical Plan, Acceptance of Work (AOW) 47 (pp. 116-183) 6. Analytical Plan, Acceptance of Work (AOW) 57 (pp.184-187) 7. Analytical Plan, Acceptance of Work (AOW) 58 (pp. 188-193) 8. Analytical Plan, Acceptance of Work (AOW) 62 (pp. 194-239) 9. Analytical Plan, Acceptance of Work (AOW) 68 (pp. 240-244) Assay Validation 10. Serial Dilution/LOD NBFAC.061117.001 (pp. 246-253) 11. Assay Validation NBFAC.061019.002 (pp. 254-259) Laboratory Reports 12. Location Searches NBFAC. 061113.001 (pp. 261-279) 13. Repository Screening NBFAC.070215.0001, NBFAC.070314.0001 to NBFAC0.70314.003 (pp. 280-359) 14. Environmental Samples NBFAC.070723.0001 (pp. 360-380) 15. Location Searches NBFAC.070727.0001, NBFAC.071102.0001, NBFAC.080828.0001 (pp. 381-440) Module 5: Molecular Analysis of Pathogen Strains and Isolates and Genetic Mutations A1 and A3 Technical Proposal and FBI SOWs: Genetic Discrimination of Bacillus anthracis Isolates Using Molecular Biological Techniques 1. Technical Proposal and FBI SOWs: Genetic Discrimination of Bacillus anthracis Isolates Using Molecular Biological Techniques (pp. 3-65) Assay Development Morph A1-A3 2. Progress Reports: May 2002-Jan 2004 (pp. 67-499)

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173 INDEX OF DOCUMENTS PROVIDED BY THE FBI Assay Development Morph A1-A3 3. Final Report (pp. 501-603) 4. Validation Study Morph A-1 Protocol (pp. 604-712) 5. Validation Study Morph A-2 Protocol (pp. 713-820) 6. Validation Study Morph A-3 Protocol (pp. 821-932) Assay Development Morph A1-A3 7. Morph A Overview PowerPoint (pp. 934-957) Repository Screening Morph A1 and A3 8. Progress and Final Reports, March 2004-Oct 2007 (pp. 959-1295) Module 6: Genetic Mutations B and D (CBI) Assay Development: Technical Proposals 1. DNA Assays for Minor Genetic Variants of Bacillus anthracis (pp. 3-76) 2. Task 1 Technical Proposal Morph B SNP (pp. 77-94) 3. Task 2 Technical Proposal Morph D Deletion (pp. 95-114) Assay Development: Progress Reports 4. Morph B (pp. 116-160) 5. Morph D (pp. 161-222) Assay Development: Standard Operating Procedures 6. Morph B Protocol (pp. 224-268) 7. Morph D Protocol (pp. 269-310) 8. Appendix 1-10 (pp. 311-867) Module 7: Genetic Mutations B and D (IITRI) Assay Development: Technical Proposals 1. Technical Proposal (pp. 3-51) 2. Task 1 DNA Assay Development – Morph B SNP (pp. 52-97) 3. Task 2 DNA Assay Development – Morph D Deletion (pp. 98-137) 4. Capabilities Brief (pp. 138-176)

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174 SCIENTIFIC APPROACHES USED TO INVESTIGATE THE ANTHRAX LETTERS Assay Development: Progress Reports 5. DNA Assays for Minor Genetic Variants Meeting Minutes 2/23/05 (pp. 178-179) 6. Task 1 Morph B SNP Progress Reports (pp. 180-215) 7. Task 2 Morph D Progress Reports (pp. 216-251) Assay Development: Validation 8. Validity Test Reports B SNP (pp. 253-408) 9. Validity Test Report D Deletion (pp. 409-661) Assay Development: Standard Operating Procedures 10. Standard Operating Procedure Real-Time PCR Assay for the Detection of the Morph B SNP (pp. 662-686) 11. Standard Operating Procedure Real-Time PCR Assay for the Detection of the Morph D Deletion (pp. 687-710) Repository Screening Morph D: Progress Reports 12. Monthly Status Reports (pp. 711-800 and 803-955) 13. FBI Kick-Off Meeting (pp. 956-996) 14. B. anthracis Morph D DNA Screening Progress Reviews (pp. 997-1016) Repository Screening Morph D: Final Reports 15. Technical Repository Screening Final Reports (pp. 1018-1134) 16. Option Period I, II, III Final Reports (pp. 1135-1212) Module 8: Genetic Mutations B and D (MRI) Assay Development: Technical Proposals 1. Volume 1 Technical Proposal (pp. 3-57) 2. Task 1 DNA Assay Development – Morph B SNP (pp. 58-80) 3. Task 2 DNA Assay Development – Morph D Deletion (pp. 81-102) Assay Development: Progress Reports 4. Task 1 Morph B SNP Progress Reports (pp. 104-170) 5. Task 2 Morph D Deletion Progress Reports (pp. 171-242)

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175 INDEX OF DOCUMENTS PROVIDED BY THE FBI Assay Development: Validation 6. Morph B SNP Assay Validity Test Report (pp. 244-260) 7. Morph D Deletion Assay Validity Test Report (pp. 261-272) Assay Development: Standard Operating Procedures 8. Extraction of DNA from Bacillus anthracis Cultures (pp. 274-281) 9. PCR-Based Assay for the Detection of Morph B SNP (pp. 282-315) 10. PCR-Based Assay for the Detection of Morph D Deletion (pp. 316-350) Assay Development: Final Reports 11. Task 1 Morph B Final Administrative Report (pp. 352-358) 12. Task 2 Morph D Final Administrative Report (pp. 359-366) 13. DNA Assay Development Morph B SNP (pp. 367-380) 14. DNA Assay Development Morph D Deletion (pp. 381-396) Repository Screening Morph D: Technical Proposals 15. Volume 1 Technical Proposal (pp. 398-435) Repository Screening Morph D: Progress Reports 16. DNA Screening of Ames Strain Anthrax Samples for Morph D (pp. 437-628) Repository Screening Morph D: Final Reports 17. Technical Repository Screening Report (pp. 630-670) 18. Technical Repository Screening Report Addendum 1 (pp. 671-675) 19. Technical Repository Screening Report Addendum 2 (pp. 676-680) Module 9: Genetic Mutation E (TIGR) Assay Development: Technical Proposals 1. LL19 Detection Assay: Validation Study Analysis Plan (pp. 3-7) 2. LL19 Detection Assay: Analysis Plan for 1060 Blind Samples (pp. 8-13)

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176 SCIENTIFIC APPROACHES USED TO INVESTIGATE THE ANTHRAX LETTERS Assay Development: Progress Reports 3. June 2004 thru Sept/Dec 2005 (see Batch 1, Module 5) Assay Development: Standard Operating Procedure 4. Opaque Assay Development SOP (pp. 16-58) Assay Development: Validation 5. B. anthracis LL19 Detection Assay: Validation Study (pp. 60-123) Assay Development: Final Report 6. Genomic Analysis of Bacillus anthracis Isolates Relevant to the Amerithrax Investigation, June 4, 2005 (Morph E (Opaque, Post/ Leahy B.s.) (see Batch 1, Module 5) Repository Screening Morph E: Final Report 7. Analysis of a Repository of Bacillus anthracis for the Presence of the LL19 Opaque Deletion Genotype (pp. 126-323) Module 10: Statistical Analysis Technical Proposal and SOW 1. Determination of the Significance of the Markers Discovered in the Evidentiary Material of Amerithrax Investigation (pp. 3-21) Final Report 2. Statistical Report of Amerithrax Data (Sept 30, 2008) (pp. 23-135) Module 11: Cross Contamination Reports 1. “Risk Assessment of Anthrax Threat Letters,” Defense R&D Canada, Technical Report DRES-TR-2001-048, September 2001 (pp. 3-36)

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177 INDEX OF DOCUMENTS PROVIDED BY THE FBI 2. “Forensic Application of Microbiological Culture Analysis to Identify Mail Intentionally Contaminated with Bacillus anthracis Spores,” D.J. Beecher, Applied Environmental Biology, Aug 2006, p. 5304-5310 (pp. 37-43) Module 12: Declassified Reports Technical Review Panel Meetings (NAS-1) 1. November 14, 2001 Technical Review Panel Meeting (pp. 3-13) Agar and Heme Analysis (NAS-1): Agar Assay Validation - BMI 2. Statement of Work B-Task-04 Chemical Process Troubleshooting (pp. 14-20) 3. SPOT Report on B-Task-04 Technical Progress Summary (pp. 21-27) Chemical and Physical Characteristics (NAS-2) (see Batch 2, Module 13) Module 13: Chemical and Physical Properties Reports 1. Determination of Concentration of Culturable Bacteria in Sample 02.57.03(Daschle) Oct 17-18, 2001 (pp. 3-7) 2. Preliminary SPOT Report on Particle Size Analysis Oct 18, 2001 (pp. 8-22) 3. SEM Images Sample A (Daschle) Oct 19, 2001 (pp. 23-28) 4. Summary of Microbiological Analyses Oct 19, 2001 (pp. 29-31) 5. Preliminary SPOT Report on Sample Analyses Oct 22, 2001 (pp. 32-57) 6. Preparation Steps and Associated Equipment Oct 25, 2001 (pp. 58-61) 7. Analysis of Silicon and Silica in Powder Samples November 21, 2001 (pp. 62-74) 8. Analysis of Silicon and Silica in Powder Samples SEM/EDS Analysis Nov 26,2001 (pp. 75-88) 9. The Analysis of Surrogate Dry Powder Bacillus Spore Product December 28, 2001 (pp. 89-98) 10. Analysis of SPS02.266.02C (Leahy) Feb 12, 2002 (pp. 99-144) 11. Summary of Sample Analysis (SPS02.266.02C) 28 Feb 02 (pp. 145-178)

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178 SCIENTIFIC APPROACHES USED TO INVESTIGATE THE ANTHRAX LETTERS Module 14: ASM Bio Defense Meeting Presentations CBI, Mr. Thomas A. Reynolds 1. The Science Behind the Amerithrax Investigation: Morph A1 and A3 Assays (pp. 3-11) MRI 2. Morphotype D Assay Development and Validation (pp. 13-33) NAU, Dr. Paul Keim 3. The Ames Strain: Frequency, Distribution, and Forensic Analysis (pp. 35-51) SNL, Dr. Joseph R. Michael 4. Elemental Microanalysis of Bacillus anthracis Spores from the Amerithrax Case (pp. 53-71) TIGR, Dr. Jacques Ravel 5. The Genomics Behind the Amerithrax Investigation (pp. 73-106) BATCH 33 1. Amerithrax Science Update – 04-26/2002 – 11/25/2005 (271 pages) 2. EC dated 2/8/2005 – Technical Review Panel Meeting Agenda, Anthrax Review Panel, Amerithrax Panel Summary 11/14/2001; 12 page PowerPoint (17 pages) 3. EC dated 12/21/2001 – Meeting of Analytical Chemistry Expert (279A-WF-222936-LAB serial 37 and 1A 579) (7 pages) 4. EC dated 2/11/2002 – Proposed Lab Analysis and R&D Strategy Analytical Flow Chart (279A-WF-22936-LAB serial 65) (5 pages) 5. EC dates 11/14/2005 – Case Agent Meeting (attached WFO Forensic & Investigation update meeting 11/05/2001) (279A-WF- 22936-LAB serial 1308 and 1A 6553) (30 pages) 6. EC dated 11/14/2005 – Scientific Review Panel Meeting June 11-22- 2002 (279A-WF-22936-LAB serial 1310 and 1A 6554) (22 pages) 3 The FBI did not assign page numbers to this batch of materials.

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179 INDEX OF DOCUMENTS PROVIDED BY THE FBI 7. EC dated 12/21/2001 – External Expert Review of Analytical Plan (279A-WF-22936-LAB serial 25 and 1A 533) (7 pages) 8. U.S. Army Medical Research Institute of Infectious Diseases, Reference Material Receipt Record (1 page) 9. 279A-WF-222936-BATTELLE Serial #914 10. 279A-WF-222936-SC118 Serial #3 (8 pages) 11. 279A-WF-222936-USAMRIID/BEI Serial #19 (7 pages) 12. 279A-WF22936-USAMRIID Serial #1418 (2 pages) 13. Dr. Ivins USAMRIID Laboratory Notebook #4010 (30 pages) 14. Incoming Shipment Records for the 8 Positive FBI Repository Samples (origin is FBIR Database) (19 pages) 15A. United States District Court Search Warrant Application and Affidavit Case#07-524-M-01 (33 pages) 15B.United States District Court Search Warrant Application and Affidavit Case#07-525-M-01 (27 pages) 15C. United States District Court Search Warrant Application and Affidavit Case#07-526-M-01 (28 pages) 15D. United States District Court Search Warrant Application and Affidavit Case#07-527-M-01 (28 pages) 15E. United States District Court Search Warrant Application and Affidavit Case#07-528-M-01 (28 pages) 15F. United States District Court Search Warrant Application and Affidavit Case#07-529-M-01 (39 pages) 16. FBI Repository Shipment Records5 (32 pages) SUPPLEMENTAL DOCUMENTS6 1. AFIP Materials related to USAMRIID Specimens October 2001 (41 pages) 2. Preparing and Shipping TSA Slants for B. Anthracis Ames (1 page) 3. FBI WFO [Washington Field Office] Report on Samples from an Overseas Site Identified by Intelligence7 (18 pages) 4 While this document was listed in the Batch 3 table of contents provided to the committee by the FBI, this document was not provided to the committee because of its security classification. 5 The FBI did not assign a name to this document. The descriptor was assigned by the committee. 6 The FBI did not assign page numbers to supplemental documents provided to the committee. 7 The FBI did not assign a name to this document. The descriptor was assigned by the committee.

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